Fridge Brilliance: The Duke has banned Pawns from entering his castle, presumably simply because they are not human. Might it not instead be that he is afraid his old Pawn will recognize him, or that another Pawn will somehow know that he did not defeat the dragon at all?
Just before the begining of the final battle, Aldous informs you that the Duke has selected your for a Super Special Mission that's very dangerous and involves being sent far away for a long time. Of course he has, and not because it's a 'great honour'. He's done it because you've seen him in the throes of madness, trying to strangle (or, depending on how you completed the quest, outright murdering) his current wife while lamenting causing the death of the previous. Plus, he may think his wife's cheating on him with you. AND, as a bonus, it might occur to him that if you manage to defeat the dragon, bad things might happen to him (as he's still bound to it) and word might get out about the deal he made, meanwhile if you choose the deal yourself, you might usurp him.
Except the Duke's attempted murder of his wife takes place in a missable/skippable side quest. At no point do you actually have to complete (or accept, or even discover the existence of) "Arousing Suspicion". The other reasons for him wanting the Arisen gone are still logical, though.
Whenever you kill a Drake in the game, they utter the phrase "the seat of heaven lies beyond". It could just be a cool line, said because they're dying and about to go to the afterlife. Or it could be a reference to the end of the game, with the Seneschal's throne as "the seat of heaven".
The Cyclops has very elephant like features. This is noteworthy because it's believed that elephant skeletons were the inspiration for the Cyclops myth. Nice little touch there, Capcom.